valosekj

import os
import glob
import hashlib
import argparse


def compute_checksum(file_path):
    with open(file_path, 'rb') as f:
        file_bytes = f.read()
    return hashlib.md5(file_bytes).hexdigest()

valosekj

# Set ITK direction from image1 to image2
#
# Usage:
#	python change_itk_orientation.py <image1> <image2>
# Example:
#	python change_itk_orientation.py sub-001_T1w.nii.gz sub-001_T1w_seg.nii.gz
#
# Jan Valosek
#

valosekj

Configuration of ssh connection

Unix and MacOS

Let's say we want to configure an ssh connection between machine alpha and beta.

1. Go to your home folder at machine alpha:

$ cd ~

valosekj

Simple workflow of collaboration in small team using git and GitHub

This gist describes example of simple workflow on repository whose changes are tracked by git and GitHub

1) Clone (download repository from GitHub to your computer)

# Go to directory where repository will be cloned (downloaded)
cd ~/Documents
# Clone repository from GitHub

valosekj

How to create and use virtual environments (venv and conda)

venv and conda are environment manager tools allowing to create virtual environments. Virtual environment separates the dependencies (Python packages) for different projects. This mean that each project can have its own dependencies. Usage of virtual environments allows you to avoid installing Python packages globally (to the system Python) which could break system tools or other projects.

venv environment

1. Create venv

MacOS or Linux (without or with site-packages)

valosekj

Run python script from shell (bash, zsh)

Sometimes, I need to call/run python script with arguments from shell. I use bash or zsh as my shell and following workaround works great for me.

Using shell wrapper

1. Some example python script which I need to run from bash:

my_python_script.py:

valosekj

Tips and hacks for plotting in python

This gist containts several useful tips, tricks and hacks for plotting of figures, plots and charts using python (matplotlib and seaborn packages).

Fix warning about matplotlib backend in PyCharm

import matplotlib
matplotlib.use('TkAgg')

valosekj

Basic shell commands

A few basic shell (bash, zsh, ...) commands for UNIX (Linux, MacOS) CLI (command-line interface)

1. File and directory manipulation commands

cd - change directory:

# change directory to /home/username/Downloads:

valosekj

Useful shell commands

This gist contains several useful shell commands which I use frequently during my work.

$0 - Get current shell

$ echo $0
zsh

valosekj

Useful string manipulation examples for bash and zsh

I need very often to modify filenames or replace/delete their parts across huge number of files. I was using sed command for these purposes but recently I have found out that all these tasks can be easily done directly in bash (or zsh) because both of them support so called string manipulation operations.

String manipulations

Define some example string:

$ file=some_file_name.txt